Exemplo n.º 1
0
def main_align(args, stdout, stderr) :
    if args.outDir is None :
        args.outDir = "."
    for fastaFile in args.input :
        pyalign.ungapFastaFile(fastaFile, fastaFile + ".ungap.tmp")
        pyalign.runMafft(fastaFile + ".ungap.tmp", fastaFile + ".tmp", args.nthreads)
        out = os.path.join(args.outDir, os.path.basename(fastaFile))
        os.rename(fastaFile + ".tmp", out)
        os.remove(fastaFile + ".ungap.tmp")
Exemplo n.º 2
0
 def test_run_000(self) :
     mod.runMafft("inputToto", "outputToto", 4)
     result = self.command
     expected = "mafft --thread 4 inputToto | awk '{if (substr($0,1,1)==\">\"){if (p){printf \"\\n\";} print $0} else printf(\"%s\",$0);p++;} END {print \"\\n\"}' > outputToto"
     self.assertEqual(result, expected)